1
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Tsuchida A, Kaneko T, Nishikawa K, Kawasaki M, Yokokawa R, Shintaku H. Opto-combinatorial indexing enables high-content transcriptomics by linking cell images and transcriptomes. LAB ON A CHIP 2024; 24:2287-2297. [PMID: 38506394 DOI: 10.1039/d3lc00866e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
We introduce a simple integrated analysis method that links cellular phenotypic behaviour with single-cell RNA sequencing (scRNA-seq) by utilizing a combination of optical indices from cells and hydrogel beads. With our method, the combinations, referred to as joint colour codes, enable the link via matching the optical combinations measured by conventional epi-fluorescence microscopy with the concatenated DNA molecular barcodes created by cell-hydrogel bead pairs and sequenced by next-generation sequencing. We validated our approach by demonstrating an accurate link between the cell image and scRNA-seq with mixed species experiments, longitudinal cell tagging by electroporation and lipofection, and gene expression analysis. Furthermore, we extended our approach to multiplexed chemical transcriptomics, which enabled us to identify distinct phenotypic behaviours in HeLa cells treated with various concentrations of paclitaxel, and determine the corresponding gene regulation associated with the formation of a multipolar spindle.
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Affiliation(s)
- Arata Tsuchida
- Cluster for Pioneering Research, RIKEN, Main Research Building 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyotodaigaku-katsura, Nishikyo-ku, Kyoto 615-8540, Japan.
| | - Taikopaul Kaneko
- Cluster for Pioneering Research, RIKEN, Main Research Building 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kaori Nishikawa
- Cluster for Pioneering Research, RIKEN, Main Research Building 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mayu Kawasaki
- Cluster for Pioneering Research, RIKEN, Main Research Building 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ryuji Yokokawa
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyotodaigaku-katsura, Nishikyo-ku, Kyoto 615-8540, Japan.
| | - Hirofumi Shintaku
- Cluster for Pioneering Research, RIKEN, Main Research Building 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Department of Micro Engineering, Graduate School of Engineering, Kyoto University, Kyotodaigaku-katsura, Nishikyo-ku, Kyoto 615-8540, Japan.
- Institute for Life and Medical Science, Kyoto University, 53 Kawara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
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2
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Gu Y, Hu Y, Zhang H, Wang S, Xu K, Su J. Single-cell RNA sequencing in osteoarthritis. Cell Prolif 2023; 56:e13517. [PMID: 37317049 PMCID: PMC10693192 DOI: 10.1111/cpr.13517] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/30/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023] Open
Abstract
Osteoarthritis is a progressive and heterogeneous joint disease with complex pathogenesis. The various phenotypes associated with each patient suggest that better subgrouping of tissues associated with genotypes in different phases of osteoarthritis may provide new insights into the onset and progression of the disease. Recently, single-cell RNA sequencing was used to describe osteoarthritis pathogenesis on a high-resolution view surpassing traditional technologies. Herein, this review summarizes the microstructural changes in articular cartilage, meniscus, synovium and subchondral bone that are mainly due to crosstalk amongst chondrocytes, osteoblasts, fibroblasts and endothelial cells during osteoarthritis progression. Next, we focus on the promising targets discovered by single-cell RNA sequencing and its potential applications in target drugs and tissue engineering. Additionally, the limited amount of research on the evaluation of bone-related biomaterials is reviewed. Based on the pre-clinical findings, we elaborate on the potential clinical values of single-cell RNA sequencing for the therapeutic strategies of osteoarthritis. Finally, a perspective on the future development of patient-centred medicine for osteoarthritis therapy combining other single-cell multi-omics technologies is discussed. This review will provide new insights into osteoarthritis pathogenesis on a cellular level and the field of applications of single-cell RNA sequencing in personalized therapeutics for osteoarthritis in the future.
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Affiliation(s)
- Yuyuan Gu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- School of MedicineShanghai UniversityShanghaiChina
| | - Yan Hu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
| | - Hao Zhang
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
| | - Sicheng Wang
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- Department of OrthopedicsShanghai Zhongye HospitalShanghaiChina
| | - Ke Xu
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
- Wenzhou Institute of Shanghai UniversityWenzhouChina
| | - Jiacan Su
- Institute of Translational MedicineShanghai UniversityShanghaiChina
- Organoid Research CenterShanghai UniversityShanghaiChina
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3
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Abdrabou A, Duong BTV, Chen K, Atwal RS, Labib M, Lin S, Angers S, Kelley SO. nuPRISM: Microfluidic Genome-Wide Phenotypic Screening Platform for Cellular Nuclei. ACS CENTRAL SCIENCE 2022; 8:1618-1626. [PMID: 36589880 PMCID: PMC9801500 DOI: 10.1021/acscentsci.2c00836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Indexed: 06/17/2023]
Abstract
Genome-wide loss-of-function screens are critical tools to identify novel genetic regulators of intracellular proteins. However, studying the changes in the organelle-specific expression profile of intracellular proteins can be challenging due to protein localization differences across the whole cell, hindering context-dependent protein expression and activity analyses. Here, we describe nuPRISM, a microfluidics chip specifically designed for large-scale isolated nuclei sorting. The new device enables rapid genome-wide loss-of-function phenotypic CRISPR-Cas9 screens directed at intranuclear targets. We deployed this technology to identify novel genetic regulators of β-catenin nuclear accumulation, a phenotypic hallmark of APC-mutated colorectal cancer. nuPRISM expands our ability to capture aberrant nuclear morphological and functional traits associated with distinctive signal transduction and subcellular localization-driven functional processes with substantial resolution and high throughput.
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Affiliation(s)
- Abdalla
M. Abdrabou
- Department
of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | - Bill T. V. Duong
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Kangfu Chen
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Randy Singh Atwal
- Department
of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | - Mahmoud Labib
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60611, United States
| | - Sichun Lin
- Terrence
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Stephane Angers
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Department
of Biochemistry, Faculty of Medicine, University
of Toronto, Toronto, Ontario M5S 1A8, Canada
- Terrence
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Shana O. Kelley
- Department
of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60611, United States
- Department
of Biomedical Engineering, Northwestern
University, Evanston, Illinois 60611, United States
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
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4
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Källberg J, Xiao W, Van Assche D, Baret JC, Taly V. Frontiers in single cell analysis: multimodal technologies and their clinical perspectives. LAB ON A CHIP 2022; 22:2403-2422. [PMID: 35703438 DOI: 10.1039/d2lc00220e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single cell multimodal analysis is at the frontier of single cell research: it defines the roles and functions of distinct cell types through simultaneous analysis to provide unprecedented insight into cellular processes. Current single cell approaches are rapidly moving toward multimodal characterizations. It replaces one-dimensional single cell analysis, for example by allowing for simultaneous measurement of transcription and post-transcriptional regulation, epigenetic modifications and/or surface protein expression. By providing deeper insights into single cell processes, multimodal single cell analyses paves the way to new understandings in various cellular processes such as cell fate decisions, physiological heterogeneity or genotype-phenotype linkages. At the forefront of this, microfluidics is key for high-throughput single cell analysis. Here, we present an overview of the recent multimodal microfluidic platforms having a potential in biomedical research, with a specific focus on their potential clinical applications.
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Affiliation(s)
- Julia Källberg
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
| | - Wenjin Xiao
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
| | - David Van Assche
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France.
| | - Jean-Christophe Baret
- University of Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac 33600, France.
- Institut Universitaire de France, Paris 75005, France
| | - Valerie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Université Paris Cité, Sorbonne Université, USPC, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
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5
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Luo X, Chen JY, Ataei M, Lee A. Microfluidic Compartmentalization Platforms for Single Cell Analysis. BIOSENSORS 2022; 12:58. [PMID: 35200319 PMCID: PMC8869497 DOI: 10.3390/bios12020058] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 12/25/2022]
Abstract
Many cellular analytical technologies measure only the average response from a cell population with an assumption that a clonal population is homogenous. The ensemble measurement often masks the difference among individual cells that can lead to misinterpretation. The advent of microfluidic technology has revolutionized single-cell analysis through precise manipulation of liquid and compartmentalizing single cells in small volumes (pico- to nano-liter). Due to its advantages from miniaturization, microfluidic systems offer an array of capabilities to study genomics, transcriptomics, and proteomics of a large number of individual cells. In this regard, microfluidic systems have emerged as a powerful technology to uncover cellular heterogeneity and expand the depth and breadth of single-cell analysis. This review will focus on recent developments of three microfluidic compartmentalization platforms (microvalve, microwell, and microdroplets) that target single-cell analysis spanning from proteomics to genomics. We also compare and contrast these three microfluidic platforms and discuss their respective advantages and disadvantages in single-cell analysis.
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Affiliation(s)
- Xuhao Luo
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA; (X.L.); (J.-Y.C.)
| | - Jui-Yi Chen
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA; (X.L.); (J.-Y.C.)
| | - Marzieh Ataei
- Department of Mechanical and Aerospace Engineering, University of California, Irvine, CA 92697, USA;
| | - Abraham Lee
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA; (X.L.); (J.-Y.C.)
- Department of Mechanical and Aerospace Engineering, University of California, Irvine, CA 92697, USA;
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6
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7
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Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, Guilliams M, Alon U, Shalek AK, Hamel R, Pfau SJ, Raj A, Quake SR, Zhang NR, Fan J, Trapnell C, Wang B, Greenwald NF, Vento-Tormo R, Santos SDM, Spencer SL, Garcia HG, Arekatla G, Gaiti F, Arbel-Goren R, Rulands S, Junker JP, Klein AM, Morris SA, Murray JI, Galloway KE, Ratz M, Romeike M. Single cell biology-a Keystone Symposia report. Ann N Y Acad Sci 2021; 1506:74-97. [PMID: 34605044 DOI: 10.1111/nyas.14692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022]
Abstract
Single cell biology has the potential to elucidate many critical biological processes and diseases, from development and regeneration to cancer. Single cell analyses are uncovering the molecular diversity of cells, revealing a clearer picture of the variation among and between different cell types. New techniques are beginning to unravel how differences in cell state-transcriptional, epigenetic, and other characteristics-can lead to different cell fates among genetically identical cells, which underlies complex processes such as embryonic development, drug resistance, response to injury, and cellular reprogramming. Single cell technologies also pose significant challenges relating to processing and analyzing vast amounts of data collected. To realize the potential of single cell technologies, new computational approaches are needed. On March 17-19, 2021, experts in single cell biology met virtually for the Keystone eSymposium "Single Cell Biology" to discuss advances both in single cell applications and technologies.
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Affiliation(s)
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California
| | - Ana I Domingos
- Department of Physiology, Anatomy & Genetics, Oxford University, Oxford, United Kingdom.,The Howard Hughes Medical Institute, New York, New York
| | - Naomi Habib
- Cell Circuits Program, Broad Institute, Cambridge, Massachusetts.,Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Homaira Hamidzada
- Toronto General Hospital Research Institute, University Health Network; Translational Biology and Engineering Program, Ted Rogers Centre for Heart Research and Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Michael S Balzer
- Renal, Electrolyte, and Hypertension Division, Department of Medicine and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Itai Yanai
- Institute for Computational Medicine, NYU Langone Health, New York, New York
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland
| | - Jessica Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts
| | - Aaron Streets
- Department of Bioengineering and Center for Computational Biology, University of California, Berkeley, Berkeley, California.,Chan Zuckerberg Biohub, San Francisco, California
| | - Long Cai
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington; and Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Clarice Kit Yee Hong
- Edison Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, Missouri.,Department of Genetics, Washington University in St. Louis, St. Louis, Missouri
| | - Leeat Keren
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | - Martin Guilliams
- Laboratory of Myeloid Cell Biology in Tissue Homeostasis and Regeneration, VIB-UGent Center for Inflammation Research, and Unit of Immunoregulation and Mucosal Immunology, VIB Inflammation Research Center, and Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Uri Alon
- Faculty of Sciences, Department of Human Biology, University of Haifa, Haifa, Israel
| | - Alex K Shalek
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts
| | - Regan Hamel
- Department of Clinical Neurosciences and NIHR Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Pfau
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts
| | - Arjun Raj
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephen R Quake
- Chan Zuckerberg Biohub, San Francisco, California.,Department of Bioengineering, Stanford University, Stanford, California.,Department of Applied Physics, Stanford University, Stanford, California
| | - Nancy R Zhang
- Graduate Group in Genomics and Computational Biology and Department of Statistics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jean Fan
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington School of Medicine; Brotman Baty Institute for Precision Medicine; and Allen Discovery Center for Cell Lineage Tracing, Seattle, Washington
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, California.,Department of Developmental Biology, Stanford University School of Medicine, Stanford, California
| | - Noah F Greenwald
- Department of Pathology, School of Medicine, Stanford University, Stanford, California
| | | | | | - Sabrina L Spencer
- Department of Biochemistry and BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Hernan G Garcia
- Department of Physics; Biophysics Graduate Group; Department of Molecular and Cell Biology; and Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, California
| | | | - Federico Gaiti
- New York Genome Center and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
| | - Steffen Rulands
- Max Planck Institute for the Physics of Complex Systems, and Center for Systems Biology Dresden, Dresden, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Allon M Klein
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts
| | - Samantha A Morris
- Department of Genetics, Washington University in St. Louis, St. Louis, Missouri.,Department of Developmental Biology and Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - John I Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kate E Galloway
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Solna, Sweden
| | - Merrit Romeike
- Max Perutz Laboratories Vienna, University of Vienna, Vienna, Austria
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8
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Davies P, Jones M, Liu J, Hebenstreit D. Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision. Brief Bioinform 2021; 22:6265204. [PMID: 33959753 PMCID: PMC8574610 DOI: 10.1093/bib/bbab148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/10/2021] [Accepted: 03/26/2021] [Indexed: 12/29/2022] Open
Abstract
RNA-seq, including single cell RNA-seq (scRNA-seq), is plagued by insufficient sensitivity and lack of precision. As a result, the full potential of (sc)RNA-seq is limited. Major factors in this respect are the presence of global bias in most datasets, which affects detection and quantitation of RNA in a length-dependent fashion. In particular, scRNA-seq is affected by technical noise and a high rate of dropouts, where the vast majority of original transcripts is not converted into sequencing reads. We discuss these biases origins and implications, bioinformatics approaches to correct for them, and how biases can be exploited to infer characteristics of the sample preparation process, which in turn can be used to improve library preparation.
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Affiliation(s)
- Philip Davies
- Daniel Hebenstreit's Research Group University of Warwick, CV4 7AL Coventry, UK
| | - Matt Jones
- Daniel Hebenstreit's Research Group University of Warwick, CV4 7AL Coventry, UK
| | - Juntai Liu
- Physics Department, University of Warwick, CV4 7AL Coventry, UK
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9
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Kim S, Dorlhiac G, Cotrim Chaves R, Zalavadia M, Streets A. Paper-thin multilayer microfluidic devices with integrated valves. LAB ON A CHIP 2021; 21:1287-1298. [PMID: 33690757 DOI: 10.1039/d0lc01217c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Integrated valve microfluidics has an unparalleled capability to automate rapid delivery of fluids at the nanoliter scale for high-throughput biological experimentation. However, multilayer soft lithography, which is used to fabricate valve-microfluidics, produces devices with a minimum thickness of around five millimeters. This form-factor limitation prevents the use of such devices in experiments with limited sample thickness tolerance such as 4-pi microscopy, stimulated Raman scattering microscopy, and many forms of optical or magnetic tweezer applications. We present a new generation of integrated valve microfluidic devices that are less than 300 μm thick, including the cover-glass substrate, that resolves the thickness limitation. This "thin-chip" was fabricated through a novel soft-lithography technique that produces on-chip micro-valves with the same functionality and reliability of traditional thick valve-microfluidic devices despite the orders of magnitude reduction in thickness. We demonstrated the advantage of using our thin-chip over traditional thick devices to automate fluid control while imaging on a high-resolution inverted microscope. First, we demonstrate that the thin-chip provides an improved signal to noise when imaging single cells with two-color stimulated Raman scattering (SRS). We then demonstrated how the thin-chip can be used to simultaneously perform on-chip magnetic manipulation of beads and fluorescent imaging. This study reveals the potential of our thin-chip in high-resolution imaging, sorting, and bead capture-based single-cell multi-omics applications.
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Affiliation(s)
- Soohong Kim
- Ningbo University, College of Food and Pharmaceutical Sciences, Ningbo, Zhejiang 315832, China
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10
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Zenhausern R, Chen CH, Yoon JY. Microfluidic sample preparation for respiratory virus detection: A review. BIOMICROFLUIDICS 2021; 15:011503. [PMID: 33643510 PMCID: PMC7889292 DOI: 10.1063/5.0041089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/28/2021] [Indexed: 05/05/2023]
Abstract
Techniques used to prepare clinical samples have been perfected for use in diagnostic testing in a variety of clinical situations, e.g., to extract, concentrate, and purify respiratory virus particles. These techniques offer a high level of purity and concentration of target samples but require significant equipment and highly trained personnel to conduct, which is difficult to achieve in resource-limited environments where rapid testing and diagnostics are crucial for proper handling of respiratory viruses. Microfluidics has popularly been utilized toward rapid virus detection in resource-limited environments, where most devices focused on detection rather than sample preparation. Initial microfluidic prototypes have been hindered by their reliance on several off-chip preprocessing steps and external laboratory equipment. Recently, sample preparation methods have also been incorporated into microfluidics to conduct the virus detection in an all-in-one, automated manner. Extraction, concentration, and purification of viruses have been demonstrated in smaller volumes of samples and reagents, with no need for specialized training or complex machinery. Recent devices show the ability to function independently and efficiently to provide rapid, automated sample preparation as well as the detection of viral samples with high efficiency. In this review, methods of microfluidic sample preparation for the isolation and purification of viral samples are discussed, limitations of current systems are summarized, and potential advances are identified.
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Affiliation(s)
- Ryan Zenhausern
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
| | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong 999077, China
| | - Jeong-Yeol Yoon
- Department of Biomedical Engineering, The University of Arizona, Tucson, Arizona 85721, USA
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11
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Altemose N, Maslan A, Rios-Martinez C, Lai A, White JA, Streets A. μDamID: A Microfluidic Approach for Joint Imaging and Sequencing of Protein-DNA Interactions in Single Cells. Cell Syst 2020; 11:354-366.e9. [PMID: 33099405 PMCID: PMC7588622 DOI: 10.1016/j.cels.2020.08.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 07/01/2020] [Accepted: 08/22/2020] [Indexed: 12/23/2022]
Abstract
DNA adenine methyltransferase identification (DamID) measures a protein's DNA-binding history by methylating adenine bases near each protein-DNA interaction site and then selectively amplifying and sequencing these methylated regions. Additionally, these interactions can be visualized using m6A-Tracer, a fluorescent protein that binds to methyladenines. Here, we combine these imaging and sequencing technologies in an integrated microfluidic platform (μDamID) that enables single-cell isolation, imaging, and sorting, followed by DamID. We use μDamID and an improved m6A-Tracer protein to generate paired imaging and sequencing data from individual human cells. We validate interactions between Lamin-B1 protein and lamina-associated domains (LADs), observe variable 3D chromatin organization and broad gene regulation patterns, and jointly measure single-cell heterogeneity in Dam expression and background methylation. μDamID provides the unique ability to compare paired imaging and sequencing data for each cell and between cells, enabling the joint analysis of the nuclear localization, sequence identity, and variability of protein-DNA interactions. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Annie Maslan
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carolina Rios-Martinez
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andre Lai
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathan A White
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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